I normally turn everything off and let the sump fill up to about 1.5-2" from the top then turn everything back on. You can always build a stand for your skimmer if need be.
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What water height should a sump be at? This is my first sump and have an adjustable baffle. I would say I am running at 10 inches or so right now. Higher...lower?
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Ummm.... Where's your skimmer? That's the most important part when it comes to determining water height.